MethylPurify 2.0-20140310

Methylation subclone detection

This script is used for predicting subclone purity.

Get Dependent data

Get the version of genome fasta that you mapped your fastqs, we support hg18 and hg19 genome fasta now.

## use built-in script
cd methylpurify/db
bash genome.sh hg18

Get Dependent software

• samtools, version larger than 0.1.18 (r982:295)

• numpy, version larger than 1.6

If your system is debian-like system, try:

sudo apt-get install python-numpy
sudo apt-get install samtools

Easy to start

Input: BAM file, this should be mapped with BSMap with -R option * BSMap

Currently, we only support hg19 and hg18 genome index mapped BAM file.

If your fastq mapping is done with hg19 index, use following command:

MethylPurify -f input.bam -b 300 -c 20 -s 50 --species hg19 -g /path/to/hg19.fa

Options

• -f: input BAM file

• -c: coverage level

• -b: genome bin size

• -s: sampling times

• –species: species genome version

• -g: species genome fasta file(correspond to –species)